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- PDB-6tky: Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tky | ||||||
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Title | Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 | ||||||
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![]() | SIGNALING PROTEIN / DOCK10 GEF CDC42 GTPase | ||||||
Function / homology | ![]() marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding ...marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / adherens junction organization / GTP-dependent protein binding / regulation of Rho protein signal transduction / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of mitotic nuclear division / phagocytosis, engulfment / nuclear migration / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / positive regulation of cytokinesis / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / B cell homeostasis / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / regulation of postsynapse assembly / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / positive regulation of GTPase activity / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of cell migration / actin filament organization / guanyl-nucleotide exchange factor activity / small monomeric GTPase / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / mitotic spindle / ubiquitin protein ligase activity / apical part of cell / intracellular protein localization / cell-cell junction / G protein activity / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barford, D. / Fan, D. / Cronin, N. / Yang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10 Authors: Fan, D. / Yang, J. / Cronin, N. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 195.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 62 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tkzC ![]() 6tm1C ![]() 2wm9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53026.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NA / Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Protein | Mass: 20958.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 53083.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 25% (w/v) PEG 3350, 200 mM potassium acetate, 8% (v/v) 1,1,1,3,3,3-Hexafluoro-2-propanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→29.83 Å / Num. obs: 49296 / % possible obs: 99.9 % / Redundancy: 7.23 % / Biso Wilson estimate: 42.35 Å2 / Rsym value: 0.126 / Net I/σ(I): 5.52 |
Reflection shell | Resolution: 2.55→2.64 Å / Num. unique obs: 5918 / Rsym value: 0.34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WM9 Resolution: 2.55→29.83 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→29.83 Å
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Refine LS restraints |
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LS refinement shell |
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